Deep Generative Models for Phylogenetic Inference with Complex Evolutionary Processes

Inference of phylogenetic trees from sequences plays a central role in understanding evolutionary relationships, with applications ranging from tracking pathogen spread to reconstructing the history of life. Conventionally, practitioners obtain posteriors over trees using likelihood-based methods like MCMC. However, likelihoods are only available for simple evolutionary models with restrictive assumptions. For realistic evolutionary models, inference using conventional methods is prohibitively expensive, inaccurate, or even impossible. In practice, practitioners settle for using as flexible a conventional method as possible, even though they expect it is misspecified. In principle, we could use simulation-based inference: simulate tree and sequence data from an evolutionary model and train a neural network to predict the posterior over trees given sequences. However it is a mathematical challenge to represent and train complex posterior distributions over trees. Here we present a flexible family of conditional generative models over trees. Our models iteratively build trees using three natural paradigms -- top-down, middle-out, or bottom-up -- and are trained using a discrete diffusion framework. For real and synthetic datasets of up to 65 taxa and >105 tokens, our models recover MCMC posteriors much more accurately than the previous state-of-the-art simulation-based method Phyloformer 2. Finally, we compare to IQ-Tree, a popular flexible-but-misspecified conventional method. Our models match its tree estimates on simple data, but on more realistic data, our method is reliably more accurate.